conda | Repository with conda recipes for LAMMPS , GROMACS , etc
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kandi X-RAY | conda Summary
Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)
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QUESTION
When a project is specified only via pyproject.toml
(i.e. no setup.{py,cfg}
files), how can it be installed in editable mode via pip
(i.e. python -m pip install -e .
)?
I tried both setuptools
and poetry
for the build system, but neither worked:
ANSWER
Answered 2022-Mar-19 at 23:06PEP 660 – Editable installs for pyproject.toml based builds defines how to build projects that only use pyproject.toml
. Build tools must implement PEP 660 for editable installs to work. You need a front-end (such as pip ≥ 21.3), backend. The statuses of some popular backends are:
QUESTION
I'm trying to study the neural-network-and-deep-learning (http://neuralnetworksanddeeplearning.com/chap1.html). Using the updated version for Python 3 by MichalDanielDobrzanski (https://github.com/MichalDanielDobrzanski/DeepLearningPython). Tried to run it in my command console and it gives an error below. I've tried uninstalling and reinstalling setuptools, theano, and numpy but none have worked thus far. Any help is very appreciated!!
Here's the full error log:
...ANSWER
Answered 2022-Feb-17 at 14:12I had the same issue and solved it downgrading numpy to version 1.20.3 by:
QUESTION
I'm trying to run a SageMaker kernel with Python 3.8 in SageMaker Studio, and the notebook appears to use a separate distribution of Python 3.7. The running app is indicated as tensorflow-2.6-cpu-py38-ubuntu20.04-v1. When I run !python3 -V
I get Python 3.8.2. However, the Python instance inside the notebook is different:
ANSWER
Answered 2022-Feb-25 at 13:00are you still facing this issue?
I am in eu-west-2 using a SageMaker Studio notebook and the TensorFlow 2.6 Python 3.8 CPU Optimized image (running app is tensorflow-2.6-cpu-py38-ubuntu20.04-v1).
When I run the below commands, I get the right outputs.
QUESTION
Does it make sense to use Conda + Poetry for a Machine Learning project? Allow me to share my (novice) understanding and please correct or enlighten me:
As far as I understand, Conda and Poetry have different purposes but are largely redundant:
- Conda is primarily a environment manager (in fact not necessarily Python), but it can also manage packages and dependencies.
- Poetry is primarily a Python package manager (say, an upgrade of pip), but it can also create and manage Python environments (say, an upgrade of Pyenv).
My idea is to use both and compartmentalize their roles: let Conda be the environment manager and Poetry the package manager. My reasoning is that (it sounds like) Conda is best for managing environments and can be used for compiling and installing non-python packages, especially CUDA drivers (for GPU capability), while Poetry is more powerful than Conda as a Python package manager.
I've managed to make this work fairly easily by using Poetry within a Conda environment. The trick is to not use Poetry to manage the Python environment: I'm not using commands like poetry shell
or poetry run
, only poetry init
, poetry install
etc (after activating the Conda environment).
For full disclosure, my environment.yml file (for Conda) looks like this:
...ANSWER
Answered 2022-Feb-14 at 10:04As I wrote in the comment, I've been using a very similar Conda + Poetry setup in a data science project for the last year, for reasons similar to yours, and it's been working fine. The great majority of my dependencies are specified in pyproject.toml
, but when there's something that's unavailable in PyPI, I add it to environment.yml
.
Some additional tips:
- Add Poetry, possibly with a version number (if needed), as a dependency in
environment.yml
, so that you get Poetry installed when you runconda env create
, along with Python and other non-PyPI dependencies. - Consider adding
conda-lock
, which gives you lock files for Conda dependencies, just like you havepoetry.lock
for Poetry dependencies.
QUESTION
For the last 5 days, I am trying to make Keras/Tensorflow packages work in R. I am using RStudio for installation and have used conda
, miniconda
, virtualenv
but it crashes each time in the end. Installing a library should not be a nightmare especially when we are talking about R (one of the best statistical languages) and TensorFlow (one of the best deep learning libraries). Can someone share a reliable way to install Keras/Tensorflow on CentOS 7?
Following are the steps I am using to install tensorflow
in RStudio.
Since RStudio simply crashes each time I run tensorflow::tf_config()
I have no way to check what is going wrong.
ANSWER
Answered 2022-Jan-16 at 00:08Perhaps my failed attempts will help someone else solve this problem; my approach:
- boot up a clean CentOS 7 vm
- install R and some dependencies
QUESTION
I just downloaded pytube (version 11.0.1) and started with this code snippet from here:
...ANSWER
Answered 2021-Nov-22 at 07:03Found this issue, pytube v11.0.1. It's a little late for me, but if no one has submitted a fix tomorrow I'll check it out.
in C:\Python38\lib\site-packages\pytube\parser.py
Change this line:
152: func_regex = re.compile(r"function\([^)]+\)")
to this:
152: func_regex = re.compile(r"function\([^)]?\)")
The issue is that the regex expects a function with an argument, but I guess youtube added some src that includes non-paramterized functions.
QUESTION
I honestly can't figure out what is happening with this error. I thought it was something in my manifest file but apparently it's not.
Note, this directory is in my Google Drive.
Here is my MANIFEST.in
file:
ANSWER
Answered 2022-Feb-07 at 15:14there are a few symptoms I would like to suggest looking into:
- There is a WARNING in your error log
SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools
. You haveMANIFEST.in
,setup.py
andsetup.cfg
probably conflicting between them. Becausesetup.py
is the build script for setuptools. It tellssetuptools
about your package (such as the name and version) as well as which code files to include. Also, An existing generated MANIFEST will be regenerated without sdist comparing its modification time to the one of MANIFEST.in or setup.py, as explained here.
Please refer to Building and Distributing Packages with Setuptools, also Configuring setup() using setup.cfg files and Quickstart for more information
- Maybe not so important, but another thing worth looking into is the fact that there are 2 different python distributions being used at different stages, as Python 3.10 is used at:
Using pip 22.0.2 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10)
(it is also in your conda dependencies) and Python 3.8 is used at:File "/Users/jespinoz/anaconda3/lib/python3.8/site-packages/conda_build/tarcheck.py", line 53, in info_files raise Exception('info/files')
which is where the error happens. So maybe another configuration conflict related to this.
QUESTION
I am trying to install conda on EMR and below is my bootstrap script, it looks like conda is getting installed but it is not getting added to environment variable. When I manually update the $PATH
variable on EMR master node, it can identify conda
. I want to use conda on Zeppelin.
I also tried adding condig into configuration like below while launching my EMR instance however I still get the below mentioned error.
...ANSWER
Answered 2022-Feb-05 at 00:17I got the conda working by modifying the script as below, emr python versions were colliding with the conda version.:
QUESTION
I am trying to set up a conda environment with python 3.10 installed. For some reason, no install commands for additional packages are working. For example, if I run conda install pandas
, I get the error:
ANSWER
Answered 2021-Oct-08 at 08:42Thats a bug in conda, you can read more about it here: https://github.com/conda/conda/issues/10969
Right now there is a PR to fix it but its not a released version. For now, just stick with
QUESTION
I work on a program for two months. Today I suddenly got an error when connecting to the database while using mysql.connector.
Interestingly, this error is not seen when running previous versions.
...ANSWER
Answered 2022-Jan-25 at 16:49I just ran into something similar. It looks like Pandas 1.4 was released on January 22, 2022: https://pandas.pydata.org/docs/dev/whatsnew/v1.4.0.html
It has an "optional" dependency on SQLAlchemy, which is required to communicate with any database other than sqlite now, as the comment by snakecharmerb mentioned. Once I added that to my requirements and installed SQLAlchemy, it resolved my problem.
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Install conda
This command installs a special version of PLUMED 2.5.1 that also includes the optional dimred module.
This command installs a special version of GROMACS 2018.6 pre-patched with PLUMED. Patching is done in runtime mode, and should by default pick the PLUMED library installed on conda in the same environment, using the command above.
This command installs a special version of LAMMPS 2019, June, pre-patched with PLUMED. Patching is done in runtime mode, and should by default pick the PLUMED library installed on conda in the same environment, using the command above.
Using conda you might also install other software that will be used during the workshop. You will likely need these python packages:.
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